#### Example configuration file
# change path, more details see documentation input files
# https://girafr.readthedocs.io/en/latest/

[config_tools] 
samtools = /data/leuven/334/vsc33470/miniconda3/bin/samtools
twoBitToFa = /staging/leuven/stg_00064/tools/ucsc/twoBitToFa
featureCounts = /data/leuven/334/vsc33470/miniconda3/envs/umi_tools/bin/featureCounts

[config_annotation]
ref_fasta = absolute_path_to_this_file/oligo_pool_plasmid.fa
structure_gtf= absolute_path_to_this_file/oligo_pool_plasmid_structure.gtf
genome = absolute_path_to_this_file/hg38.2bit # 2bit file downloaded from UCSC
genome_gtf = absolute_path_to_this_file/Homo_sapiens.GRCh38.93.gtf # gtf file from ensembl

[config_gRNA_mutation]
gRNA_bam_file = absolute_path_to_this_file/bam_file
filtered_barcode= absolute_path_to_this_file/barcode.tsv # unzipped
output_dir= absolute_path_to_output_folder
auto = True 
pool = True

[config_detect_editing_effect]
gRNA_region = absolute_path_to_this_file/gRNA_region_coordinates_hg38.txt # required by editing_effect command
expression_bam_file = absolute_path_to_this_file/possorted_genome_bam.bam # output from cellranger 
filtered_barcode = absolute_path_to_this_file/barcode.tsv # unzipped
cell_file = absolute_path_to_this_file/cells.gRNA.txt # cell assignment results by gRNA_mutation command or protospacer_call_per_cell by cellranger
output_dir = absolute_path_to_output_folder
window_size = 81 # recommended 
